Fixes for inline parameters. Better error handling/reporting for cwltest.

Author: Peter Amstutz

cwltool/cwltest.py

@@ -110,12 +110,12 @@ def run_test(args, i, t):
                 _logger.warn(t.get("doc"))
                 failed = True
             _logger.warn("%s expected %s\n%s      got %s", key,
-                                                            t.get(key),
+                                                            json.dumps(t.get(key), indent=4, sort_keys=True),
                                                             " " * len(key),
-                                                            out.get(key))
+                                                            json.dumps(out.get(key), indent=4, sort_keys=True))
 
     if outdir:
-        shutil.rmtree(outdir)
+        shutil.rmtree(outdir, True)
 
     if failed:
         return 1

cwltool/draft2tool.py

@@ -32,7 +32,8 @@ class ExpressionJob(object):
         def run(self, **kwargs):
             try:
                 self.output_callback(self.builder.do_eval(self.script), "success")
-            except Exception:
+            except Exception as e:
+                _logger.warn("Failed to evaluate expression:\n%s", e, exc_info=(e if kwargs.get('debug') else False))
                 self.output_callback({}, "permanentFail")
 
     def job(self, joborder, input_basedir, output_callback, **kwargs):

cwltool/expression.py

@@ -96,20 +96,21 @@ class DR(object):
 
 def next_seg(remain, obj):
     if remain:
-        print remain
         m = segment_re.match(remain)
         if m.group(0)[0] == '.':
             return next_seg(remain[m.end(0):], obj[m.group(0)[1:]])
-        else:
+        elif m.group(0)[1] in ("'", '"'):
             key = m.group(0)[2:-2].replace("\\'", "'").replace('\\"', '"')
             return next_seg(remain[m.end(0):], obj[key])
+        else:
+            key = m.group(0)[1:-1]
+            return next_seg(remain[m.end(0):], obj[int(key)])
     else:
         return obj
 
 def param_interpolate(ex, obj, strip=True):
     m = param_re.search(ex)
     if m:
-        print "=", m.group(0), "/", m.group(0)[m.end(1) - m.start(0):-1]
         leaf = next_seg(m.group(0)[m.end(1) - m.start(0):-1], obj[m.group(1)])
         if strip and len(ex.strip()) == len(m.group(0)):
             return leaf

cwltool/main.py

@@ -373,7 +373,7 @@ def main(args=None,
     if args.conformance_test:
         loader = Loader({})
     else:
-        loader = Loader({"id": "@id", "path": {"@type": "@id"}})
+        loader = Loader({"path": {"@type": "@id"}})
 
     if len(args.job_order) == 1 and args.job_order[0][0] != "-":
         job_order_file = args.job_order[0]
@@ -414,11 +414,18 @@ def main(args=None,
                 job_order_object = {}
 
             job_order_object.update({namemap[k]: v for k,v in cmd_line.items()})
+
             _logger.debug("Parsed job order from command line: %s", job_order_object)
         else:
             job_order_object = None
 
-    if not job_order_object:
+    for inp in t.tool["inputs"]:
+        if "default" in inp and (not job_order_object or shortname(inp["id"]) not in job_order_object):
+            if not job_order_object:
+                job_order_object = {}
+            job_order_object[shortname(inp["id"])] = inp["default"]
+
+    if not job_order_object and len(t.tool["inputs"]) > 0:
         parser.print_help()
         if toolparser:
             print "\nOptions for %s " % args.workflow

tests/test_examples.py

@@ -59,7 +59,7 @@ def test_params(self):
 
         self.assertEqual(expr.param_interpolate("$(foo['b ar'].baz)", inputs), 2)
         self.assertEqual(expr.param_interpolate("$(foo['b\\'ar'].baz)", inputs), True)
-        self.assertEqual(expr.param_interpolate("$(foo[\"b\\'ar\"].baz)", inputs), True)
+        self.assertEqual(expr.param_interpolate("$(foo[\"b'ar\"].baz)", inputs), True)
         self.assertEqual(expr.param_interpolate("$(foo['b\\\"ar'].baz)", inputs), None)